Our software solutions


Proline
(Proteomics & Mass Spectrometry software suite)

description: Proline is a platform which can perform a set of proteomics data computations and present the obtained results through a user-friendly GUIs. Proline algorithms focus on:  result validation (using custom filters and target decoy analysis), merge/comparison of datasets, label-free quantification (spectral count and LC-MS analyses). Mascot and OMSSA results are currently supported because of the nature of the Proline data persistence layer, which is based on a relational database extended with flexible JSON annotations. Other search engines will further be supported. Using an efficient, structured and extensible persistence layer allows Proline to handle large-scale proteomic studies issued from many different analytical strategies. Proline is developed in the context of the ProFI consortium.

available at: http://proline.profiproteomics.fr/

DAPAR/ProStaR

description: For statistical analyses of quantitative proteomics data EDyP developed DAPAR and ProStaR. These software tools perform the statistical analysis of label-free XIC-based quantitative proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser.

DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages.

reference: Wieczorek S., Combes F., et al. (2016). “DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics.” Bioinformatics. Accepted for publication, September 2016.

available at: http://www.bioconductor.org/

PredAlgo (prediction of subcellular localisation in green algae)

description: PredAlgo is a new sequence analysis tool, dedicated to the prediction of protein subcellular localization in green algae. It uses a neural network trained with carefuly curated sets of Chlamydomonas reinhardtii proteins. PredAlgo predicts the localization to one of three compartments: the mitochondrion, the chloroplast, the secretory pathway within the cell.

reference: Tardif M., Atteia A., et al. (2012). “PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae.” Mol Biol Evol. doi: 10.1093/molbev/mss178

available at: https://giavap-genomes.ibpc.fr/cgi-bin/predalgodb.perl?page=main (web-application)

get more  : standalone version

hEIDI (grouping and exploring identification results)

description: In order to manage and combine both identifications and semi-quantitative data related to multiple LC-MS/MS analyses, we have developed a unique software environment called hEIDI (handy Exploration and Integration of Data and Identifications). Through a user-friendly interface, hEIDI allows results from multiple analyses to be compiled in order to retrieve a joint list of non-redundant protein groups. Moreover, hEIDI allows direct comparison of collections of analyses using protein group similarities computed based on the Dice coefficient, while ensuring protein grouping consistency and the computation of various spectral counts metrics. hEIDI also ensures that validated results are compliant with MIAPE guidelines, as all information related to samples and results is stored in an appropriate relational database. Finally, validated results generated within hEIDI can be easily exported in the PRIDE format for subsequent publication.

reference: Hesse A.M., Dupierris V., et al.  (2016). “hEIDI: An intuitive application tool to organize and treat large-scale proteomics data.” J Proteome Res. 2016 Aug 25. PMID: 27560970.

available at: http://biodev.extra.cea.fr/docs/heidi

IRMa (automated and manual validation of Mascot identifications results)

description: IRMa reads MASCOT® result and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” and sub-sets. User can then manually validate or invalidate peptides, information consistency (sequence coverage rate, score but also proteins hits maintenance) being ensured by IRMa. Finally, this application also offers multiple export possibilities, including a database export of identification results.

reference: Dupierris V., Masselon CM., et al. (2009). “A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa.” Bioinformatics 25(15): 1980-1.

available at: http://biodev.extra.cea.fr/docs/irma/doku.php

ePims (lab activity management)

description: ePIMS (experiment Proteomic Information Management System) is a LIMS dedicated to proteomics. ePIMS is an modular infrastructure which helps laboratories organize, trace and manage efficiently  electronic data associated with mass spectrometry-based proteomic analysis as well as samples informations. Source code and distribution packages are freely available on request (contact Christophe Bruley or Véronique Dupierris).

reference: Dupierris V., Barthe D., Bruley C. “ePIMS: un LIMS pour la gestion des données de spectrométrie de masse” Spectra Analyse. 2009 Sept-Oct ; 269

available at: ePims is deployed by ASA http://www.advancedsolutionsaccelerator.com/

PepLine (genomes annotation using MS/MS data – proteogenomics)

description: Pepline is a fully automated software to map MS/MS fragmentation spectra of enzymatic digested peptides to genomic DNA sequences. The approach is based on Peptide Sequence Tags (PSTs) resulting from partial interpretation of the MS/MS spectra.

reference: Ferro M., Tardif M., et al. (2008). “PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences.” J Proteome Res 7(5): 1873-83.

available at: ftp server has been changed…and will be soon available, please come back later or contact us